Starting phenix.real_space_refine on Tue Feb 20 16:50:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g74_29796/02_2024/8g74_29796.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g74_29796/02_2024/8g74_29796.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g74_29796/02_2024/8g74_29796.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g74_29796/02_2024/8g74_29796.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g74_29796/02_2024/8g74_29796.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g74_29796/02_2024/8g74_29796.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 920 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 124 5.16 5 C 17494 2.51 5 N 4549 2.21 5 O 5376 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27543 Number of models: 1 Model: "" Number of chains: 19 Chain: "E" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 877 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "A" Number of atoms: 8367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1071, 8367 Classifications: {'peptide': 1071} Link IDs: {'PTRANS': 57, 'TRANS': 1013} Chain breaks: 4 Chain: "B" Number of atoms: 8382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1073, 8382 Classifications: {'peptide': 1073} Link IDs: {'PTRANS': 57, 'TRANS': 1015} Chain breaks: 4 Chain: "C" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 877 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "D" Number of atoms: 8382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1073, 8382 Classifications: {'peptide': 1073} Link IDs: {'PTRANS': 57, 'TRANS': 1015} Chain breaks: 4 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "D" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 14.35, per 1000 atoms: 0.52 Number of scatterers: 27543 At special positions: 0 Unit cell: (163.52, 148.19, 208.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 124 16.00 O 5376 8.00 N 4549 7.00 C 17494 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.04 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.06 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.05 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.06 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.03 Simple disulfide: pdb=" SG CYS D 15 " - pdb=" SG CYS D 136 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.04 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.05 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.05 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.02 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.02 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.02 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 343 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A1074 " " NAG B1301 " - " ASN B 234 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 331 " " NAG B1304 " - " ASN B 343 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B 717 " " NAG B1310 " - " ASN B1074 " " NAG D1301 " - " ASN D 61 " " NAG D1302 " - " ASN D 122 " " NAG D1303 " - " ASN D 282 " " NAG D1304 " - " ASN D 331 " " NAG D1305 " - " ASN D 616 " " NAG D1306 " - " ASN D 657 " " NAG D1307 " - " ASN D 709 " " NAG D1308 " - " ASN D1074 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 801 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN B1098 " " NAG L 1 " - " ASN B1134 " " NAG M 1 " - " ASN D 717 " " NAG N 1 " - " ASN D 801 " " NAG O 1 " - " ASN D1098 " " NAG P 1 " - " ASN D1134 " Time building additional restraints: 11.89 Conformation dependent library (CDL) restraints added in 5.1 seconds 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6430 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 54 sheets defined 23.1% alpha, 26.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.49 Creating SS restraints... Processing helix chain 'E' and resid 86 through 90 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.878A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.601A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 759 removed outlier: 6.861A pdb=" N SER A 758 " --> pdb=" O GLN A 755 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE A 759 " --> pdb=" O TYR A 756 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 755 through 759' Processing helix chain 'A' and resid 760 through 783 removed outlier: 3.604A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.582A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 4.073A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.392A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.028A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 386 through 390 removed outlier: 3.603A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.659A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.581A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.695A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 4.433A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.937A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.511A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.766A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.312A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.114A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 64 removed outlier: 3.891A pdb=" N LYS C 64 " --> pdb=" O ASN C 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 61 through 64' Processing helix chain 'C' and resid 86 through 90 Processing helix chain 'D' and resid 294 through 304 Processing helix chain 'D' and resid 338 through 343 Processing helix chain 'D' and resid 365 through 370 Processing helix chain 'D' and resid 406 through 410 Processing helix chain 'D' and resid 416 through 422 Processing helix chain 'D' and resid 438 through 443 removed outlier: 3.658A pdb=" N SER D 443 " --> pdb=" O ASN D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 505 Processing helix chain 'D' and resid 737 through 743 Processing helix chain 'D' and resid 746 through 754 Processing helix chain 'D' and resid 755 through 757 No H-bonds generated for 'chain 'D' and resid 755 through 757' Processing helix chain 'D' and resid 758 through 783 removed outlier: 3.574A pdb=" N ASP D 775 " --> pdb=" O ALA D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 825 Processing helix chain 'D' and resid 866 through 885 Processing helix chain 'D' and resid 886 through 891 removed outlier: 3.553A pdb=" N ALA D 890 " --> pdb=" O TRP D 886 " (cutoff:3.500A) Processing helix chain 'D' and resid 897 through 908 Processing helix chain 'D' and resid 912 through 919 removed outlier: 3.975A pdb=" N LEU D 916 " --> pdb=" O THR D 912 " (cutoff:3.500A) Processing helix chain 'D' and resid 919 through 941 removed outlier: 3.602A pdb=" N THR D 941 " --> pdb=" O SER D 937 " (cutoff:3.500A) Processing helix chain 'D' and resid 942 through 944 No H-bonds generated for 'chain 'D' and resid 942 through 944' Processing helix chain 'D' and resid 945 through 965 removed outlier: 3.945A pdb=" N VAL D 951 " --> pdb=" O LYS D 947 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU D 962 " --> pdb=" O ALA D 958 " (cutoff:3.500A) Processing helix chain 'D' and resid 966 through 968 No H-bonds generated for 'chain 'D' and resid 966 through 968' Processing helix chain 'D' and resid 976 through 984 Processing helix chain 'D' and resid 985 through 1033 removed outlier: 4.776A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) Processing helix chain 'D' and resid 1140 through 1147 removed outlier: 3.962A pdb=" N GLU D1144 " --> pdb=" O PRO D1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.155A pdb=" N GLY E 10 " --> pdb=" O THR E 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'E' and resid 57 through 59 removed outlier: 6.550A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N VAL E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N MET E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.341A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.933A pdb=" N ARG D 567 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA D 575 " --> pdb=" O GLY D 566 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ASP D 574 " --> pdb=" O ILE D 587 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N GLU D 324 " --> pdb=" O ASN D 540 " (cutoff:3.500A) removed outlier: 8.961A pdb=" N ASN D 542 " --> pdb=" O GLU D 324 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 50 through 55 Processing sheet with id=AA7, first strand: chain 'A' and resid 68 through 69 removed outlier: 3.731A pdb=" N ARG A 78 " --> pdb=" O HIS A 69 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA9, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.668A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 311 through 317 removed outlier: 6.793A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.642A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.077A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.801A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB6, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.504A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.069A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.036A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.036A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.412A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AC3, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.438A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.293A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.813A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 68 through 69 removed outlier: 3.654A pdb=" N ARG B 78 " --> pdb=" O HIS B 69 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 153 through 157 removed outlier: 3.617A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 311 through 318 removed outlier: 5.154A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.525A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N PHE B 565 " --> pdb=" O PHE D 43 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.078A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.674A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD4, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.614A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.087A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.863A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.817A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.468A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.395A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AE2, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.166A pdb=" N GLY C 10 " --> pdb=" O THR C 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 57 through 59 removed outlier: 6.566A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N VAL C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N MET C 34 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 28 through 30 removed outlier: 8.212A pdb=" N ASN D 61 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N TYR D 269 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N PHE D 201 " --> pdb=" O ASP D 228 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASP D 228 " --> pdb=" O PHE D 201 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE D 203 " --> pdb=" O LEU D 226 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 47 through 55 removed outlier: 3.938A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 68 through 70 removed outlier: 3.697A pdb=" N ARG D 78 " --> pdb=" O HIS D 69 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 84 through 85 Processing sheet with id=AE8, first strand: chain 'D' and resid 84 through 85 removed outlier: 3.634A pdb=" N GLY D 103 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ALA D 243 " --> pdb=" O ILE D 101 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ILE D 101 " --> pdb=" O ALA D 243 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ARG D 102 " --> pdb=" O ASN D 121 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER D 172 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL D 130 " --> pdb=" O PHE D 168 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE D 168 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 311 through 319 removed outlier: 6.926A pdb=" N VAL D 595 " --> pdb=" O THR D 315 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N ASN D 317 " --> pdb=" O GLY D 593 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLY D 593 " --> pdb=" O ASN D 317 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY D 594 " --> pdb=" O GLN D 613 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 354 through 358 removed outlier: 3.687A pdb=" N LYS D 378 " --> pdb=" O VAL D 433 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 361 through 362 removed outlier: 6.537A pdb=" N CYS D 361 " --> pdb=" O CYS D 525 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AF4, first strand: chain 'D' and resid 473 through 474 removed outlier: 3.583A pdb=" N TYR D 489 " --> pdb=" O TYR D 473 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 654 through 655 removed outlier: 6.154A pdb=" N GLU D 654 " --> pdb=" O ALA D 694 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N THR D 696 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE D 670 " --> pdb=" O ILE D 666 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 711 through 715 removed outlier: 3.659A pdb=" N THR D1076 " --> pdb=" O SER D1097 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 718 through 728 removed outlier: 5.712A pdb=" N TYR D1067 " --> pdb=" O HIS D1048 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N HIS D1048 " --> pdb=" O TYR D1067 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 733 through 736 removed outlier: 4.418A pdb=" N LYS D 733 " --> pdb=" O LEU D 861 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 1120 through 1125 removed outlier: 4.351A pdb=" N ALA D1087 " --> pdb=" O SER D1123 " (cutoff:3.500A) 1100 hydrogen bonds defined for protein. 3003 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.98 Time building geometry restraints manager: 12.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 4476 1.29 - 1.42: 7438 1.42 - 1.56: 16089 1.56 - 1.69: 4 1.69 - 1.82: 160 Bond restraints: 28167 Sorted by residual: bond pdb=" C PRO B 899 " pdb=" O PRO B 899 " ideal model delta sigma weight residual 1.237 1.155 0.082 1.26e-02 6.30e+03 4.23e+01 bond pdb=" N VAL B1068 " pdb=" CA VAL B1068 " ideal model delta sigma weight residual 1.454 1.489 -0.035 7.70e-03 1.69e+04 2.05e+01 bond pdb=" N VAL D1068 " pdb=" CA VAL D1068 " ideal model delta sigma weight residual 1.457 1.491 -0.034 9.00e-03 1.23e+04 1.40e+01 bond pdb=" CA PRO D 25 " pdb=" C PRO D 25 " ideal model delta sigma weight residual 1.514 1.534 -0.020 5.50e-03 3.31e+04 1.34e+01 bond pdb=" C ALA B 903 " pdb=" O ALA B 903 " ideal model delta sigma weight residual 1.237 1.195 0.041 1.17e-02 7.31e+03 1.25e+01 ... (remaining 28162 not shown) Histogram of bond angle deviations from ideal: 98.46 - 105.62: 563 105.62 - 112.78: 15056 112.78 - 119.94: 9583 119.94 - 127.11: 12882 127.11 - 134.27: 253 Bond angle restraints: 38337 Sorted by residual: angle pdb=" C ASP D 571 " pdb=" CA ASP D 571 " pdb=" CB ASP D 571 " ideal model delta sigma weight residual 110.04 119.71 -9.67 1.51e+00 4.39e-01 4.11e+01 angle pdb=" N ILE A 805 " pdb=" CA ILE A 805 " pdb=" C ILE A 805 " ideal model delta sigma weight residual 113.71 108.85 4.86 9.50e-01 1.11e+00 2.62e+01 angle pdb=" C CYS A 291 " pdb=" N ALA A 292 " pdb=" CA ALA A 292 " ideal model delta sigma weight residual 122.56 113.85 8.71 1.72e+00 3.38e-01 2.57e+01 angle pdb=" CA MET B 902 " pdb=" C MET B 902 " pdb=" N ALA B 903 " ideal model delta sigma weight residual 117.30 122.76 -5.46 1.16e+00 7.43e-01 2.21e+01 angle pdb=" N SER D 982 " pdb=" CA SER D 982 " pdb=" C SER D 982 " ideal model delta sigma weight residual 112.87 107.39 5.48 1.20e+00 6.94e-01 2.09e+01 ... (remaining 38332 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.33: 16373 25.33 - 50.66: 859 50.66 - 75.98: 102 75.98 - 101.31: 41 101.31 - 126.64: 14 Dihedral angle restraints: 17389 sinusoidal: 7378 harmonic: 10011 Sorted by residual: dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual 93.00 16.95 76.05 1 1.00e+01 1.00e-02 7.29e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -161.97 75.97 1 1.00e+01 1.00e-02 7.27e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -154.53 68.53 1 1.00e+01 1.00e-02 6.09e+01 ... (remaining 17386 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.299: 4460 0.299 - 0.597: 7 0.597 - 0.896: 1 0.896 - 1.195: 0 1.195 - 1.493: 1 Chirality restraints: 4469 Sorted by residual: chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B 282 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -0.91 -1.49 2.00e-01 2.50e+01 5.58e+01 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.51e+01 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 5.19e+01 ... (remaining 4466 not shown) Planarity restraints: 4953 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1304 " 0.357 2.00e-02 2.50e+03 3.06e-01 1.17e+03 pdb=" C7 NAG A1304 " -0.088 2.00e-02 2.50e+03 pdb=" C8 NAG A1304 " 0.143 2.00e-02 2.50e+03 pdb=" N2 NAG A1304 " -0.544 2.00e-02 2.50e+03 pdb=" O7 NAG A1304 " 0.132 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D1303 " 0.358 2.00e-02 2.50e+03 3.04e-01 1.15e+03 pdb=" C7 NAG D1303 " -0.092 2.00e-02 2.50e+03 pdb=" C8 NAG D1303 " 0.174 2.00e-02 2.50e+03 pdb=" N2 NAG D1303 " -0.534 2.00e-02 2.50e+03 pdb=" O7 NAG D1303 " 0.094 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1302 " -0.269 2.00e-02 2.50e+03 2.24e-01 6.28e+02 pdb=" C7 NAG A1302 " 0.075 2.00e-02 2.50e+03 pdb=" C8 NAG A1302 " -0.183 2.00e-02 2.50e+03 pdb=" N2 NAG A1302 " 0.373 2.00e-02 2.50e+03 pdb=" O7 NAG A1302 " 0.005 2.00e-02 2.50e+03 ... (remaining 4950 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.13: 25 2.13 - 2.82: 8394 2.82 - 3.52: 36396 3.52 - 4.21: 64594 4.21 - 4.90: 111614 Nonbonded interactions: 221023 Sorted by model distance: nonbonded pdb=" O SER B 373 " pdb=" CD1 TRP B 436 " model vdw 1.439 3.260 nonbonded pdb=" CE1 PHE D 374 " pdb=" CE3 TRP D 436 " model vdw 1.493 3.640 nonbonded pdb=" OD1 ASN D 394 " pdb=" CG GLU D 516 " model vdw 1.546 3.440 nonbonded pdb=" CD ARG D 328 " pdb=" OD2 ASP D 578 " model vdw 1.550 3.440 nonbonded pdb=" CE1 HIS D 519 " pdb=" NH2 ARG D 567 " model vdw 1.688 3.340 ... (remaining 221018 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 14 through 676 or resid 690 through 827 or resid 855 throu \ gh 1147 or resid 1301 through 1307)) selection = (chain 'D' and (resid 14 through 676 or resid 690 through 827 or resid 855 throu \ gh 1147 or resid 1301 through 1307)) } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.160 Construct map_model_manager: 0.020 Extract box with map and model: 21.660 Check model and map are aligned: 0.400 Set scattering table: 0.240 Process input model: 76.450 Find NCS groups from input model: 2.100 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6526 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 28167 Z= 0.374 Angle : 0.864 10.105 38337 Z= 0.524 Chirality : 0.064 1.493 4469 Planarity : 0.011 0.306 4917 Dihedral : 15.492 126.640 10836 Min Nonbonded Distance : 1.439 Molprobity Statistics. All-atom Clashscore : 20.53 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.43 % Favored : 96.40 % Rotamer: Outliers : 1.20 % Allowed : 13.63 % Favored : 85.17 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.14), residues: 3413 helix: 1.26 (0.20), residues: 690 sheet: -0.20 (0.17), residues: 842 loop : -1.15 (0.14), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 886 HIS 0.021 0.002 HIS B 207 PHE 0.039 0.002 PHE B 400 TYR 0.032 0.002 TYR D 423 ARG 0.011 0.001 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 307 time to evaluate : 3.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 34 MET cc_start: 0.0926 (tmt) cc_final: 0.0541 (mpt) REVERT: A 59 PHE cc_start: 0.5550 (m-10) cc_final: 0.5296 (m-80) REVERT: A 266 TYR cc_start: 0.5140 (m-80) cc_final: 0.4813 (m-10) REVERT: A 281 GLU cc_start: 0.4694 (OUTLIER) cc_final: 0.4290 (tt0) REVERT: A 374 PHE cc_start: 0.5432 (m-80) cc_final: 0.4833 (m-80) REVERT: A 429 PHE cc_start: 0.8079 (t80) cc_final: 0.7832 (t80) REVERT: A 436 TRP cc_start: 0.6233 (p90) cc_final: 0.6022 (p90) REVERT: A 528 LYS cc_start: 0.7560 (ttmm) cc_final: 0.6588 (ttpt) REVERT: A 530 SER cc_start: 0.7674 (p) cc_final: 0.7365 (t) REVERT: A 779 GLN cc_start: 0.7915 (tt0) cc_final: 0.7160 (tp-100) REVERT: A 921 LYS cc_start: 0.7392 (tppt) cc_final: 0.6850 (mttp) REVERT: A 954 GLN cc_start: 0.8194 (mt0) cc_final: 0.7977 (mt0) REVERT: A 1010 GLN cc_start: 0.7387 (mm110) cc_final: 0.6428 (pt0) REVERT: A 1092 GLU cc_start: 0.7430 (pt0) cc_final: 0.7175 (pt0) REVERT: A 1119 ASN cc_start: 0.7325 (m-40) cc_final: 0.7056 (m110) REVERT: A 1125 ASN cc_start: 0.6018 (m-40) cc_final: 0.5286 (p0) REVERT: B 153 MET cc_start: 0.1511 (tpp) cc_final: -0.1148 (mtp) REVERT: B 269 TYR cc_start: 0.7676 (m-80) cc_final: 0.7423 (m-80) REVERT: B 304 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.6955 (mtpt) REVERT: B 338 PHE cc_start: 0.4173 (OUTLIER) cc_final: 0.3756 (m-10) REVERT: B 537 LYS cc_start: 0.6420 (tttt) cc_final: 0.5836 (tmtt) REVERT: B 546 LEU cc_start: 0.6092 (tt) cc_final: 0.5706 (mp) REVERT: B 947 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.8121 (mttt) REVERT: B 994 ASP cc_start: 0.6414 (t70) cc_final: 0.6097 (t70) REVERT: D 153 MET cc_start: -0.0577 (mtm) cc_final: -0.1174 (mmm) REVERT: D 192 PHE cc_start: 0.6489 (m-80) cc_final: 0.6070 (m-80) REVERT: D 535 LYS cc_start: 0.5987 (mttt) cc_final: 0.5779 (mtmm) REVERT: D 583 GLU cc_start: 0.6801 (pt0) cc_final: 0.6448 (mp0) REVERT: D 780 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7390 (mt-10) REVERT: D 854 LYS cc_start: 0.4199 (ptpt) cc_final: 0.3776 (tptt) REVERT: D 1002 GLN cc_start: 0.7225 (tt0) cc_final: 0.6985 (tt0) REVERT: D 1017 GLU cc_start: 0.7171 (tt0) cc_final: 0.6959 (tt0) REVERT: D 1113 GLN cc_start: 0.8208 (mm110) cc_final: 0.7918 (mm-40) REVERT: D 1138 TYR cc_start: 0.7626 (t80) cc_final: 0.7341 (t80) outliers start: 36 outliers final: 16 residues processed: 337 average time/residue: 1.0935 time to fit residues: 448.4976 Evaluate side-chains 221 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 201 time to evaluate : 2.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 353 TRP Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 645 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 289 optimal weight: 10.0000 chunk 259 optimal weight: 0.0020 chunk 144 optimal weight: 0.0970 chunk 88 optimal weight: 4.9990 chunk 175 optimal weight: 8.9990 chunk 138 optimal weight: 0.8980 chunk 268 optimal weight: 20.0000 chunk 104 optimal weight: 0.5980 chunk 163 optimal weight: 7.9990 chunk 200 optimal weight: 0.2980 chunk 311 optimal weight: 8.9990 overall best weight: 0.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 32 ASN E 58 GLN A 69 HIS A 188 ASN ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN A 354 ASN A 519 HIS A 613 GLN A 764 ASN A 784 GLN A 914 ASN A 960 ASN A1005 GLN A1010 GLN A1048 HIS A1101 HIS A1106 GLN B 69 HIS B 137 ASN B 188 ASN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN B 762 GLN B 804 GLN B 901 GLN B 907 ASN B 914 ASN B 935 GLN B1101 HIS B1119 ASN ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 HIS D 121 ASN D 519 HIS ** D 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 613 GLN D 641 ASN D 762 GLN D 784 GLN D 901 GLN D 960 ASN D 969 ASN D 978 ASN D1101 HIS D1113 GLN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6546 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 28167 Z= 0.188 Angle : 0.634 11.157 38337 Z= 0.320 Chirality : 0.047 0.338 4469 Planarity : 0.005 0.080 4917 Dihedral : 8.204 90.043 4722 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.64 % Favored : 97.30 % Rotamer: Outliers : 2.49 % Allowed : 14.06 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.14), residues: 3413 helix: 1.70 (0.20), residues: 704 sheet: 0.03 (0.17), residues: 838 loop : -1.13 (0.14), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 436 HIS 0.004 0.001 HIS B 66 PHE 0.030 0.002 PHE A 400 TYR 0.020 0.001 TYR B 266 ARG 0.005 0.000 ARG D 355 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 210 time to evaluate : 2.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 34 MET cc_start: 0.0854 (tmt) cc_final: 0.0497 (mpt) REVERT: A 59 PHE cc_start: 0.5597 (m-10) cc_final: 0.5367 (m-80) REVERT: A 153 MET cc_start: 0.0339 (ptp) cc_final: -0.0375 (pp-130) REVERT: A 266 TYR cc_start: 0.5190 (m-80) cc_final: 0.4916 (m-10) REVERT: A 374 PHE cc_start: 0.5745 (m-80) cc_final: 0.5284 (m-80) REVERT: A 528 LYS cc_start: 0.7621 (ttmm) cc_final: 0.7279 (ttmm) REVERT: A 530 SER cc_start: 0.7723 (p) cc_final: 0.7410 (t) REVERT: A 754 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8195 (mp) REVERT: A 779 GLN cc_start: 0.7889 (tt0) cc_final: 0.7174 (tp-100) REVERT: A 921 LYS cc_start: 0.7283 (tppt) cc_final: 0.6795 (mttp) REVERT: A 954 GLN cc_start: 0.8152 (mt0) cc_final: 0.7930 (mt0) REVERT: A 1010 GLN cc_start: 0.7322 (mm-40) cc_final: 0.6421 (pt0) REVERT: A 1092 GLU cc_start: 0.7436 (pt0) cc_final: 0.7168 (pt0) REVERT: A 1119 ASN cc_start: 0.7156 (m-40) cc_final: 0.6852 (m110) REVERT: B 53 ASP cc_start: 0.6681 (t0) cc_final: 0.6382 (t0) REVERT: B 153 MET cc_start: 0.1358 (tpp) cc_final: -0.1157 (mtp) REVERT: B 269 TYR cc_start: 0.7727 (m-80) cc_final: 0.7165 (m-10) REVERT: B 338 PHE cc_start: 0.4319 (OUTLIER) cc_final: 0.3835 (m-10) REVERT: B 534 VAL cc_start: 0.7770 (OUTLIER) cc_final: 0.7399 (m) REVERT: B 537 LYS cc_start: 0.6706 (tttt) cc_final: 0.6046 (tmtt) REVERT: B 577 ARG cc_start: 0.6543 (ttm110) cc_final: 0.6258 (ptp-110) REVERT: B 719 THR cc_start: 0.8687 (OUTLIER) cc_final: 0.8350 (t) REVERT: B 787 GLN cc_start: 0.8086 (mt0) cc_final: 0.7882 (mt0) REVERT: B 960 ASN cc_start: 0.8064 (OUTLIER) cc_final: 0.7825 (m-40) REVERT: B 994 ASP cc_start: 0.6346 (t70) cc_final: 0.6069 (t70) REVERT: C 82 MET cc_start: -0.0194 (mmm) cc_final: -0.0741 (ptp) REVERT: D 126 VAL cc_start: 0.6119 (OUTLIER) cc_final: 0.5752 (t) REVERT: D 153 MET cc_start: -0.0672 (mtm) cc_final: -0.1181 (mmm) REVERT: D 211 ASN cc_start: 0.2294 (OUTLIER) cc_final: 0.1885 (m-40) REVERT: D 229 LEU cc_start: 0.6718 (OUTLIER) cc_final: 0.6500 (mp) REVERT: D 238 PHE cc_start: 0.5694 (p90) cc_final: 0.5464 (p90) REVERT: D 535 LYS cc_start: 0.5977 (mttt) cc_final: 0.5753 (mtmm) REVERT: D 583 GLU cc_start: 0.6676 (pt0) cc_final: 0.6340 (mp0) REVERT: D 604 THR cc_start: 0.7219 (m) cc_final: 0.6889 (m) REVERT: D 780 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7316 (mt-10) REVERT: D 854 LYS cc_start: 0.4205 (ptpt) cc_final: 0.3757 (tptt) REVERT: D 1002 GLN cc_start: 0.7187 (tt0) cc_final: 0.6974 (tt0) REVERT: D 1138 TYR cc_start: 0.7608 (t80) cc_final: 0.7334 (t80) outliers start: 75 outliers final: 29 residues processed: 273 average time/residue: 1.0950 time to fit residues: 365.7158 Evaluate side-chains 217 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 180 time to evaluate : 2.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 738 CYS Chi-restraints excluded: chain D residue 974 SER Chi-restraints excluded: chain D residue 1136 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 173 optimal weight: 0.2980 chunk 96 optimal weight: 5.9990 chunk 259 optimal weight: 9.9990 chunk 212 optimal weight: 3.9990 chunk 85 optimal weight: 0.0870 chunk 312 optimal weight: 0.8980 chunk 337 optimal weight: 3.9990 chunk 277 optimal weight: 0.9990 chunk 309 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 250 optimal weight: 30.0000 overall best weight: 1.0562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 901 GLN A1002 GLN B 66 HIS B 245 HIS B 613 GLN B1005 GLN ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 ASN ** D 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 641 ASN D1088 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6650 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 28167 Z= 0.214 Angle : 0.609 11.697 38337 Z= 0.308 Chirality : 0.046 0.273 4469 Planarity : 0.005 0.067 4917 Dihedral : 6.106 58.943 4694 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.81 % Favored : 97.10 % Rotamer: Outliers : 3.12 % Allowed : 14.00 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.14), residues: 3413 helix: 1.85 (0.20), residues: 695 sheet: 0.04 (0.16), residues: 870 loop : -1.09 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 436 HIS 0.005 0.001 HIS A1088 PHE 0.030 0.002 PHE D 541 TYR 0.022 0.001 TYR B1067 ARG 0.008 0.001 ARG A 577 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 209 time to evaluate : 2.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 34 MET cc_start: 0.1160 (tmt) cc_final: 0.0820 (mpt) REVERT: A 70 VAL cc_start: 0.1694 (OUTLIER) cc_final: 0.1477 (m) REVERT: A 153 MET cc_start: 0.0601 (ptp) cc_final: -0.0310 (pp-130) REVERT: A 266 TYR cc_start: 0.5419 (m-80) cc_final: 0.5219 (m-10) REVERT: A 281 GLU cc_start: 0.5142 (OUTLIER) cc_final: 0.4812 (tt0) REVERT: A 528 LYS cc_start: 0.7679 (ttmm) cc_final: 0.7403 (ttmm) REVERT: A 530 SER cc_start: 0.7741 (p) cc_final: 0.7382 (t) REVERT: A 564 GLN cc_start: 0.6939 (mt0) cc_final: 0.6462 (mt0) REVERT: A 673 SER cc_start: 0.7956 (p) cc_final: 0.7697 (t) REVERT: A 754 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8336 (mp) REVERT: A 758 SER cc_start: 0.8241 (m) cc_final: 0.8021 (p) REVERT: A 779 GLN cc_start: 0.7923 (tt0) cc_final: 0.7170 (tp40) REVERT: A 921 LYS cc_start: 0.7343 (tppt) cc_final: 0.6813 (mttp) REVERT: A 987 PRO cc_start: 0.7108 (Cg_exo) cc_final: 0.6741 (Cg_endo) REVERT: A 1010 GLN cc_start: 0.7405 (mm-40) cc_final: 0.6546 (pt0) REVERT: A 1092 GLU cc_start: 0.7347 (pt0) cc_final: 0.7058 (pt0) REVERT: B 32 PHE cc_start: 0.6221 (m-10) cc_final: 0.6010 (m-10) REVERT: B 53 ASP cc_start: 0.6780 (t0) cc_final: 0.6376 (t0) REVERT: B 153 MET cc_start: 0.1710 (tpp) cc_final: -0.1097 (mtp) REVERT: B 201 PHE cc_start: 0.6944 (t80) cc_final: 0.6461 (t80) REVERT: B 269 TYR cc_start: 0.7780 (m-80) cc_final: 0.7163 (m-80) REVERT: B 271 GLN cc_start: 0.7039 (mt0) cc_final: 0.6274 (mp10) REVERT: B 534 VAL cc_start: 0.7855 (OUTLIER) cc_final: 0.7608 (m) REVERT: B 719 THR cc_start: 0.8781 (OUTLIER) cc_final: 0.8416 (t) REVERT: B 740 MET cc_start: 0.8073 (tpp) cc_final: 0.7791 (tpp) REVERT: B 994 ASP cc_start: 0.6688 (t70) cc_final: 0.6369 (t70) REVERT: B 1005 GLN cc_start: 0.7893 (OUTLIER) cc_final: 0.7455 (mt0) REVERT: B 1010 GLN cc_start: 0.7669 (mm110) cc_final: 0.6836 (pt0) REVERT: C 82 MET cc_start: -0.0206 (mmm) cc_final: -0.0574 (mtt) REVERT: D 126 VAL cc_start: 0.6136 (OUTLIER) cc_final: 0.5727 (t) REVERT: D 153 MET cc_start: -0.0657 (mtm) cc_final: -0.1135 (mmm) REVERT: D 229 LEU cc_start: 0.6617 (OUTLIER) cc_final: 0.6404 (mp) REVERT: D 238 PHE cc_start: 0.6003 (p90) cc_final: 0.5711 (p90) REVERT: D 535 LYS cc_start: 0.6198 (mttt) cc_final: 0.5653 (mtmm) REVERT: D 583 GLU cc_start: 0.6738 (pt0) cc_final: 0.6410 (mp0) REVERT: D 734 THR cc_start: 0.8343 (m) cc_final: 0.8086 (p) REVERT: D 780 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7374 (mt-10) REVERT: D 796 ASP cc_start: 0.7156 (p0) cc_final: 0.6924 (t0) REVERT: D 854 LYS cc_start: 0.4417 (ptpt) cc_final: 0.3926 (tptt) REVERT: D 907 ASN cc_start: 0.8214 (m-40) cc_final: 0.7929 (m-40) REVERT: D 957 GLN cc_start: 0.7384 (OUTLIER) cc_final: 0.7010 (mt0) REVERT: D 1002 GLN cc_start: 0.7368 (tt0) cc_final: 0.7107 (tt0) REVERT: D 1017 GLU cc_start: 0.7264 (tt0) cc_final: 0.6703 (mt-10) REVERT: D 1138 TYR cc_start: 0.7586 (t80) cc_final: 0.7310 (t80) outliers start: 94 outliers final: 40 residues processed: 283 average time/residue: 1.0185 time to fit residues: 355.3982 Evaluate side-chains 238 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 189 time to evaluate : 3.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 121 ASN Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 957 GLN Chi-restraints excluded: chain D residue 1136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 308 optimal weight: 2.9990 chunk 234 optimal weight: 5.9990 chunk 161 optimal weight: 30.0000 chunk 34 optimal weight: 50.0000 chunk 148 optimal weight: 6.9990 chunk 209 optimal weight: 0.9990 chunk 313 optimal weight: 2.9990 chunk 331 optimal weight: 1.9990 chunk 163 optimal weight: 9.9990 chunk 296 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A1002 GLN A1005 GLN A1125 ASN A1135 ASN B 66 HIS B 914 ASN B1088 HIS C 32 ASN D 121 ASN ** D 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 641 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6743 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 28167 Z= 0.357 Angle : 0.688 8.825 38337 Z= 0.351 Chirality : 0.050 0.280 4469 Planarity : 0.005 0.060 4917 Dihedral : 6.113 54.373 4689 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.49 % Favored : 96.45 % Rotamer: Outliers : 4.39 % Allowed : 13.46 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.14), residues: 3413 helix: 1.34 (0.20), residues: 702 sheet: 0.07 (0.17), residues: 886 loop : -1.28 (0.13), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 886 HIS 0.007 0.002 HIS D1088 PHE 0.028 0.002 PHE D 541 TYR 0.038 0.002 TYR A1067 ARG 0.005 0.001 ARG D 44 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 200 time to evaluate : 3.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 34 MET cc_start: 0.1731 (tmt) cc_final: 0.1395 (mpt) REVERT: A 70 VAL cc_start: 0.1761 (OUTLIER) cc_final: 0.1542 (m) REVERT: A 127 VAL cc_start: 0.6920 (OUTLIER) cc_final: 0.6558 (m) REVERT: A 281 GLU cc_start: 0.5160 (OUTLIER) cc_final: 0.4815 (tt0) REVERT: A 528 LYS cc_start: 0.7650 (ttmm) cc_final: 0.7376 (ttmm) REVERT: A 530 SER cc_start: 0.7765 (p) cc_final: 0.7539 (p) REVERT: A 564 GLN cc_start: 0.6725 (mt0) cc_final: 0.6229 (mt0) REVERT: A 761 THR cc_start: 0.8163 (OUTLIER) cc_final: 0.7953 (m) REVERT: A 779 GLN cc_start: 0.7989 (tt0) cc_final: 0.7201 (tp40) REVERT: A 921 LYS cc_start: 0.7603 (tppt) cc_final: 0.6980 (mtmp) REVERT: A 987 PRO cc_start: 0.7540 (Cg_exo) cc_final: 0.7221 (Cg_endo) REVERT: A 1092 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.7005 (pt0) REVERT: B 30 ASN cc_start: 0.6489 (t0) cc_final: 0.6197 (t0) REVERT: B 52 GLN cc_start: 0.7490 (tp40) cc_final: 0.7260 (tp40) REVERT: B 53 ASP cc_start: 0.6807 (t0) cc_final: 0.6238 (t70) REVERT: B 54 LEU cc_start: 0.7435 (mt) cc_final: 0.7163 (mm) REVERT: B 153 MET cc_start: 0.1202 (tpp) cc_final: -0.1379 (mtt) REVERT: B 201 PHE cc_start: 0.6772 (t80) cc_final: 0.6395 (t80) REVERT: B 237 ARG cc_start: 0.6592 (ptp-110) cc_final: 0.6369 (ptp-110) REVERT: B 271 GLN cc_start: 0.7184 (mt0) cc_final: 0.6769 (mt0) REVERT: B 338 PHE cc_start: 0.4336 (OUTLIER) cc_final: 0.3874 (m-10) REVERT: B 740 MET cc_start: 0.8057 (tpp) cc_final: 0.7841 (tpp) REVERT: B 814 LYS cc_start: 0.7084 (OUTLIER) cc_final: 0.6305 (pptt) REVERT: B 1010 GLN cc_start: 0.7698 (mm110) cc_final: 0.6790 (pt0) REVERT: D 45 SER cc_start: 0.7823 (p) cc_final: 0.7621 (t) REVERT: D 52 GLN cc_start: 0.7330 (OUTLIER) cc_final: 0.6819 (mm-40) REVERT: D 126 VAL cc_start: 0.6481 (OUTLIER) cc_final: 0.6044 (t) REVERT: D 153 MET cc_start: -0.0756 (mtm) cc_final: -0.1264 (mmp) REVERT: D 211 ASN cc_start: 0.2201 (OUTLIER) cc_final: 0.1847 (m-40) REVERT: D 237 ARG cc_start: 0.7062 (mtt180) cc_final: 0.6577 (mtm180) REVERT: D 304 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.6879 (mmtm) REVERT: D 361 CYS cc_start: 0.5743 (OUTLIER) cc_final: 0.4401 (p) REVERT: D 534 VAL cc_start: 0.7152 (OUTLIER) cc_final: 0.6921 (t) REVERT: D 535 LYS cc_start: 0.6526 (mttt) cc_final: 0.6043 (mtmm) REVERT: D 565 PHE cc_start: 0.4965 (m-80) cc_final: 0.4677 (m-10) REVERT: D 583 GLU cc_start: 0.6777 (pt0) cc_final: 0.6519 (mp0) REVERT: D 735 SER cc_start: 0.8196 (t) cc_final: 0.7633 (p) REVERT: D 780 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7415 (mt-10) REVERT: D 854 LYS cc_start: 0.4669 (ptpt) cc_final: 0.4157 (tptt) REVERT: D 978 ASN cc_start: 0.7434 (t0) cc_final: 0.6646 (m-40) REVERT: D 988 GLU cc_start: 0.7405 (tp30) cc_final: 0.6893 (tt0) REVERT: D 1002 GLN cc_start: 0.7440 (tt0) cc_final: 0.7148 (tt0) REVERT: D 1017 GLU cc_start: 0.7318 (tt0) cc_final: 0.7111 (tt0) REVERT: D 1038 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.7833 (mppt) REVERT: D 1125 ASN cc_start: 0.7331 (m-40) cc_final: 0.7092 (p0) REVERT: D 1138 TYR cc_start: 0.7642 (t80) cc_final: 0.7401 (t80) outliers start: 132 outliers final: 55 residues processed: 301 average time/residue: 1.0662 time to fit residues: 392.7554 Evaluate side-chains 252 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 183 time to evaluate : 3.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 304 LYS Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 957 GLN Chi-restraints excluded: chain D residue 974 SER Chi-restraints excluded: chain D residue 1038 LYS Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 276 optimal weight: 6.9990 chunk 188 optimal weight: 0.8980 chunk 4 optimal weight: 20.0000 chunk 246 optimal weight: 0.6980 chunk 136 optimal weight: 10.0000 chunk 282 optimal weight: 0.7980 chunk 229 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 169 optimal weight: 0.7980 chunk 297 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 914 ASN A1010 GLN B 66 HIS ** D 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 641 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 28167 Z= 0.177 Angle : 0.563 8.868 38337 Z= 0.288 Chirality : 0.045 0.255 4469 Planarity : 0.004 0.056 4917 Dihedral : 5.514 59.744 4689 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.58 % Favored : 97.36 % Rotamer: Outliers : 3.03 % Allowed : 15.23 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.14), residues: 3413 helix: 1.66 (0.20), residues: 694 sheet: 0.06 (0.16), residues: 925 loop : -1.17 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 436 HIS 0.003 0.001 HIS B1088 PHE 0.029 0.001 PHE D 541 TYR 0.038 0.001 TYR A1067 ARG 0.008 0.000 ARG A 577 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 190 time to evaluate : 3.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 34 MET cc_start: 0.1670 (tmt) cc_final: 0.1340 (mpt) REVERT: A 70 VAL cc_start: 0.1691 (OUTLIER) cc_final: 0.1475 (m) REVERT: A 127 VAL cc_start: 0.6897 (OUTLIER) cc_final: 0.6550 (m) REVERT: A 191 GLU cc_start: 0.5889 (mt-10) cc_final: 0.5531 (mp0) REVERT: A 281 GLU cc_start: 0.5129 (OUTLIER) cc_final: 0.4844 (tt0) REVERT: A 528 LYS cc_start: 0.7692 (ttmm) cc_final: 0.6829 (ttpt) REVERT: A 564 GLN cc_start: 0.6743 (mt0) cc_final: 0.6205 (mt0) REVERT: A 779 GLN cc_start: 0.7934 (tt0) cc_final: 0.7168 (tp40) REVERT: A 921 LYS cc_start: 0.7460 (tppt) cc_final: 0.6857 (mttp) REVERT: A 987 PRO cc_start: 0.7404 (Cg_exo) cc_final: 0.7068 (Cg_endo) REVERT: A 1010 GLN cc_start: 0.7361 (mm-40) cc_final: 0.6542 (pt0) REVERT: A 1092 GLU cc_start: 0.7241 (pt0) cc_final: 0.6907 (pt0) REVERT: B 30 ASN cc_start: 0.6375 (t0) cc_final: 0.6133 (t0) REVERT: B 53 ASP cc_start: 0.6606 (t0) cc_final: 0.6017 (t70) REVERT: B 54 LEU cc_start: 0.7516 (mt) cc_final: 0.7304 (mm) REVERT: B 68 ILE cc_start: 0.3283 (OUTLIER) cc_final: 0.2423 (mm) REVERT: B 153 MET cc_start: 0.0834 (tpp) cc_final: -0.1458 (mtt) REVERT: B 201 PHE cc_start: 0.6701 (t80) cc_final: 0.6420 (t80) REVERT: B 237 ARG cc_start: 0.6626 (ptp-110) cc_final: 0.6419 (ptp-110) REVERT: B 271 GLN cc_start: 0.7191 (mt0) cc_final: 0.6775 (mt0) REVERT: B 578 ASP cc_start: 0.7884 (t0) cc_final: 0.7650 (t70) REVERT: B 735 SER cc_start: 0.8323 (t) cc_final: 0.7847 (p) REVERT: B 740 MET cc_start: 0.8012 (tpp) cc_final: 0.7693 (tpp) REVERT: B 960 ASN cc_start: 0.8114 (OUTLIER) cc_final: 0.7851 (m-40) REVERT: B 990 GLU cc_start: 0.7158 (mt-10) cc_final: 0.6488 (tm-30) REVERT: B 1010 GLN cc_start: 0.7598 (mm110) cc_final: 0.6780 (pt0) REVERT: C 82 MET cc_start: -0.0188 (mmm) cc_final: -0.0679 (ptp) REVERT: D 45 SER cc_start: 0.7731 (p) cc_final: 0.7477 (t) REVERT: D 153 MET cc_start: -0.0703 (mtm) cc_final: -0.1219 (mmp) REVERT: D 211 ASN cc_start: 0.2246 (OUTLIER) cc_final: 0.1922 (m-40) REVERT: D 237 ARG cc_start: 0.6998 (mtt180) cc_final: 0.6526 (mtm180) REVERT: D 361 CYS cc_start: 0.5709 (OUTLIER) cc_final: 0.4667 (p) REVERT: D 535 LYS cc_start: 0.6511 (mttt) cc_final: 0.5983 (mtmm) REVERT: D 565 PHE cc_start: 0.4846 (m-80) cc_final: 0.4561 (m-10) REVERT: D 583 GLU cc_start: 0.6763 (pt0) cc_final: 0.6452 (mp0) REVERT: D 735 SER cc_start: 0.8152 (t) cc_final: 0.7682 (p) REVERT: D 854 LYS cc_start: 0.4624 (ptpt) cc_final: 0.4101 (tptt) REVERT: D 978 ASN cc_start: 0.7338 (t0) cc_final: 0.6550 (m-40) REVERT: D 988 GLU cc_start: 0.7327 (tp30) cc_final: 0.6907 (tt0) REVERT: D 1002 GLN cc_start: 0.7431 (tt0) cc_final: 0.7121 (tt0) REVERT: D 1017 GLU cc_start: 0.7220 (tt0) cc_final: 0.7017 (tt0) REVERT: D 1125 ASN cc_start: 0.7367 (m-40) cc_final: 0.7024 (p0) outliers start: 91 outliers final: 42 residues processed: 262 average time/residue: 1.0716 time to fit residues: 344.7867 Evaluate side-chains 225 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 176 time to evaluate : 3.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 738 CYS Chi-restraints excluded: chain D residue 787 GLN Chi-restraints excluded: chain D residue 957 GLN Chi-restraints excluded: chain D residue 974 SER Chi-restraints excluded: chain D residue 985 ASP Chi-restraints excluded: chain D residue 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 111 optimal weight: 0.9990 chunk 298 optimal weight: 0.0670 chunk 65 optimal weight: 8.9990 chunk 194 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 331 optimal weight: 0.5980 chunk 275 optimal weight: 0.7980 chunk 153 optimal weight: 20.0000 chunk 27 optimal weight: 20.0000 chunk 109 optimal weight: 4.9990 chunk 174 optimal weight: 0.4980 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN B 66 HIS D 207 HIS ** D 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 641 ASN D 762 GLN D 969 ASN D1071 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 28167 Z= 0.158 Angle : 0.547 11.107 38337 Z= 0.278 Chirality : 0.044 0.270 4469 Planarity : 0.004 0.054 4917 Dihedral : 5.132 55.398 4687 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.75 % Favored : 97.19 % Rotamer: Outliers : 3.29 % Allowed : 14.83 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.14), residues: 3413 helix: 1.85 (0.20), residues: 696 sheet: 0.13 (0.16), residues: 912 loop : -1.11 (0.14), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 64 HIS 0.018 0.001 HIS B 66 PHE 0.031 0.001 PHE D 541 TYR 0.018 0.001 TYR D 351 ARG 0.006 0.000 ARG A 577 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 187 time to evaluate : 2.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 34 MET cc_start: 0.1640 (tmt) cc_final: 0.1317 (mpt) REVERT: A 70 VAL cc_start: 0.1693 (OUTLIER) cc_final: 0.1476 (m) REVERT: A 127 VAL cc_start: 0.6906 (OUTLIER) cc_final: 0.6564 (m) REVERT: A 191 GLU cc_start: 0.5821 (mt-10) cc_final: 0.5487 (mp0) REVERT: A 528 LYS cc_start: 0.7723 (ttmm) cc_final: 0.6862 (ttpt) REVERT: A 564 GLN cc_start: 0.6717 (mt0) cc_final: 0.6186 (mt0) REVERT: A 754 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8442 (mp) REVERT: A 779 GLN cc_start: 0.7877 (tt0) cc_final: 0.7151 (tp-100) REVERT: A 921 LYS cc_start: 0.7409 (tppt) cc_final: 0.6835 (mttp) REVERT: A 987 PRO cc_start: 0.7394 (Cg_exo) cc_final: 0.7006 (Cg_endo) REVERT: A 1010 GLN cc_start: 0.7334 (mm-40) cc_final: 0.6519 (pt0) REVERT: A 1092 GLU cc_start: 0.7233 (pt0) cc_final: 0.6949 (pt0) REVERT: B 30 ASN cc_start: 0.6434 (t0) cc_final: 0.6185 (t0) REVERT: B 53 ASP cc_start: 0.6624 (t0) cc_final: 0.6036 (t70) REVERT: B 153 MET cc_start: 0.0701 (tpp) cc_final: -0.1496 (mtt) REVERT: B 201 PHE cc_start: 0.6751 (t80) cc_final: 0.6528 (t80) REVERT: B 271 GLN cc_start: 0.7194 (mt0) cc_final: 0.6788 (mt0) REVERT: B 338 PHE cc_start: 0.4370 (OUTLIER) cc_final: 0.3759 (m-10) REVERT: B 574 ASP cc_start: 0.6444 (OUTLIER) cc_final: 0.5992 (m-30) REVERT: B 719 THR cc_start: 0.8761 (OUTLIER) cc_final: 0.8394 (t) REVERT: B 735 SER cc_start: 0.8330 (t) cc_final: 0.7836 (p) REVERT: B 740 MET cc_start: 0.8070 (tpp) cc_final: 0.7721 (tpp) REVERT: B 754 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.7941 (mp) REVERT: B 814 LYS cc_start: 0.6950 (OUTLIER) cc_final: 0.6678 (mmtp) REVERT: B 960 ASN cc_start: 0.8124 (OUTLIER) cc_final: 0.7857 (m-40) REVERT: B 990 GLU cc_start: 0.7170 (mt-10) cc_final: 0.6529 (tm-30) REVERT: B 1010 GLN cc_start: 0.7661 (mm110) cc_final: 0.6791 (pt0) REVERT: C 82 MET cc_start: -0.0269 (mmm) cc_final: -0.0701 (ptp) REVERT: D 45 SER cc_start: 0.7746 (p) cc_final: 0.7488 (t) REVERT: D 153 MET cc_start: -0.0681 (mtm) cc_final: -0.1214 (mmp) REVERT: D 211 ASN cc_start: 0.2229 (OUTLIER) cc_final: 0.1892 (m-40) REVERT: D 237 ARG cc_start: 0.6979 (mtt180) cc_final: 0.6493 (mtm180) REVERT: D 361 CYS cc_start: 0.5797 (OUTLIER) cc_final: 0.4690 (p) REVERT: D 535 LYS cc_start: 0.6560 (mttt) cc_final: 0.5995 (mtmm) REVERT: D 565 PHE cc_start: 0.4817 (m-80) cc_final: 0.4512 (m-10) REVERT: D 583 GLU cc_start: 0.6657 (pt0) cc_final: 0.6374 (mp0) REVERT: D 604 THR cc_start: 0.7741 (m) cc_final: 0.7446 (m) REVERT: D 735 SER cc_start: 0.8209 (t) cc_final: 0.7756 (p) REVERT: D 854 LYS cc_start: 0.4589 (ptpt) cc_final: 0.4076 (tptt) REVERT: D 978 ASN cc_start: 0.7301 (t0) cc_final: 0.6524 (m-40) REVERT: D 988 GLU cc_start: 0.7388 (tp30) cc_final: 0.6985 (mt-10) REVERT: D 1002 GLN cc_start: 0.7456 (tt0) cc_final: 0.7175 (tt0) REVERT: D 1038 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8183 (tppt) REVERT: D 1125 ASN cc_start: 0.7399 (m-40) cc_final: 0.7027 (p0) outliers start: 99 outliers final: 46 residues processed: 271 average time/residue: 1.1123 time to fit residues: 369.1841 Evaluate side-chains 239 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 181 time to evaluate : 2.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 738 CYS Chi-restraints excluded: chain D residue 740 MET Chi-restraints excluded: chain D residue 964 LYS Chi-restraints excluded: chain D residue 974 SER Chi-restraints excluded: chain D residue 985 ASP Chi-restraints excluded: chain D residue 1038 LYS Chi-restraints excluded: chain D residue 1136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 319 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 189 optimal weight: 4.9990 chunk 242 optimal weight: 20.0000 chunk 187 optimal weight: 1.9990 chunk 279 optimal weight: 30.0000 chunk 185 optimal weight: 1.9990 chunk 330 optimal weight: 0.5980 chunk 206 optimal weight: 3.9990 chunk 201 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A1106 GLN B 66 HIS D 148 ASN D 641 ASN D 762 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6734 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 28167 Z= 0.237 Angle : 0.592 9.869 38337 Z= 0.302 Chirality : 0.046 0.274 4469 Planarity : 0.005 0.055 4917 Dihedral : 5.201 59.917 4687 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.31 % Favored : 96.57 % Rotamer: Outliers : 3.22 % Allowed : 15.06 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.57 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.14), residues: 3413 helix: 1.70 (0.20), residues: 700 sheet: 0.06 (0.16), residues: 898 loop : -1.12 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 64 HIS 0.006 0.001 HIS B 69 PHE 0.034 0.002 PHE D 541 TYR 0.023 0.001 TYR A1067 ARG 0.006 0.000 ARG A 577 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 188 time to evaluate : 3.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 34 MET cc_start: 0.1908 (tmt) cc_final: 0.1623 (mpt) REVERT: A 70 VAL cc_start: 0.1713 (OUTLIER) cc_final: 0.1507 (m) REVERT: A 127 VAL cc_start: 0.6926 (OUTLIER) cc_final: 0.6573 (m) REVERT: A 359 SER cc_start: 0.7148 (p) cc_final: 0.6741 (m) REVERT: A 528 LYS cc_start: 0.7674 (ttmm) cc_final: 0.6809 (ttpt) REVERT: A 564 GLN cc_start: 0.6673 (mt0) cc_final: 0.6113 (mt0) REVERT: A 565 PHE cc_start: 0.6244 (m-80) cc_final: 0.6039 (m-10) REVERT: A 779 GLN cc_start: 0.7945 (tt0) cc_final: 0.7171 (tp40) REVERT: A 921 LYS cc_start: 0.7504 (tppt) cc_final: 0.6882 (mttp) REVERT: A 987 PRO cc_start: 0.7551 (Cg_exo) cc_final: 0.7186 (Cg_endo) REVERT: A 1092 GLU cc_start: 0.7255 (pt0) cc_final: 0.6960 (pt0) REVERT: B 30 ASN cc_start: 0.6430 (t0) cc_final: 0.6158 (t0) REVERT: B 53 ASP cc_start: 0.6739 (t0) cc_final: 0.6240 (t0) REVERT: B 68 ILE cc_start: 0.3685 (OUTLIER) cc_final: 0.3352 (pp) REVERT: B 153 MET cc_start: 0.0850 (tpp) cc_final: -0.1451 (mtt) REVERT: B 202 LYS cc_start: 0.6888 (mttt) cc_final: 0.6659 (mttp) REVERT: B 271 GLN cc_start: 0.7182 (mt0) cc_final: 0.6774 (mt0) REVERT: B 338 PHE cc_start: 0.4406 (OUTLIER) cc_final: 0.3775 (m-10) REVERT: B 574 ASP cc_start: 0.6613 (OUTLIER) cc_final: 0.6180 (m-30) REVERT: B 719 THR cc_start: 0.8801 (OUTLIER) cc_final: 0.8409 (t) REVERT: B 735 SER cc_start: 0.8326 (t) cc_final: 0.7817 (p) REVERT: B 740 MET cc_start: 0.8084 (tpp) cc_final: 0.7795 (tpp) REVERT: B 814 LYS cc_start: 0.6980 (OUTLIER) cc_final: 0.6703 (mmtp) REVERT: B 990 GLU cc_start: 0.7182 (mt-10) cc_final: 0.6497 (tm-30) REVERT: B 1010 GLN cc_start: 0.7657 (mm110) cc_final: 0.6826 (pt0) REVERT: C 82 MET cc_start: -0.0297 (mmm) cc_final: -0.0765 (ptp) REVERT: D 153 MET cc_start: -0.0668 (mtm) cc_final: -0.1242 (mmp) REVERT: D 237 ARG cc_start: 0.6973 (mtt180) cc_final: 0.6446 (mtm180) REVERT: D 361 CYS cc_start: 0.5699 (OUTLIER) cc_final: 0.4541 (p) REVERT: D 535 LYS cc_start: 0.6775 (mttt) cc_final: 0.6113 (mtmm) REVERT: D 565 PHE cc_start: 0.4851 (m-80) cc_final: 0.4572 (m-10) REVERT: D 735 SER cc_start: 0.8233 (t) cc_final: 0.7732 (p) REVERT: D 854 LYS cc_start: 0.4657 (ptpt) cc_final: 0.4146 (tptt) REVERT: D 978 ASN cc_start: 0.7486 (t0) cc_final: 0.6673 (m-40) REVERT: D 983 ARG cc_start: 0.6625 (ttp80) cc_final: 0.6328 (ttm170) REVERT: D 988 GLU cc_start: 0.7338 (tp30) cc_final: 0.7010 (mt-10) REVERT: D 1038 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.7835 (mppt) outliers start: 97 outliers final: 55 residues processed: 269 average time/residue: 1.1224 time to fit residues: 365.9151 Evaluate side-chains 240 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 176 time to evaluate : 2.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 740 MET Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 957 GLN Chi-restraints excluded: chain D residue 974 SER Chi-restraints excluded: chain D residue 985 ASP Chi-restraints excluded: chain D residue 1038 LYS Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 204 optimal weight: 0.9990 chunk 132 optimal weight: 0.0980 chunk 197 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 64 optimal weight: 10.0000 chunk 210 optimal weight: 3.9990 chunk 225 optimal weight: 30.0000 chunk 163 optimal weight: 30.0000 chunk 30 optimal weight: 0.1980 chunk 259 optimal weight: 5.9990 chunk 300 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN B 66 HIS B1002 GLN D 641 ASN D 762 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 28167 Z= 0.187 Angle : 0.556 10.951 38337 Z= 0.284 Chirality : 0.045 0.262 4469 Planarity : 0.004 0.055 4917 Dihedral : 4.975 58.157 4687 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.96 % Favored : 96.95 % Rotamer: Outliers : 2.93 % Allowed : 15.72 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.14), residues: 3413 helix: 1.80 (0.20), residues: 699 sheet: 0.05 (0.16), residues: 914 loop : -1.08 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 64 HIS 0.003 0.001 HIS A1064 PHE 0.033 0.001 PHE D 541 TYR 0.019 0.001 TYR A1067 ARG 0.005 0.000 ARG A 577 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 191 time to evaluate : 2.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 34 MET cc_start: 0.1946 (tmt) cc_final: 0.1663 (mpt) REVERT: A 70 VAL cc_start: 0.1603 (OUTLIER) cc_final: 0.1394 (m) REVERT: A 127 VAL cc_start: 0.6927 (OUTLIER) cc_final: 0.6578 (m) REVERT: A 191 GLU cc_start: 0.5959 (mt-10) cc_final: 0.5535 (mp0) REVERT: A 359 SER cc_start: 0.7203 (p) cc_final: 0.6810 (m) REVERT: A 528 LYS cc_start: 0.7672 (ttmm) cc_final: 0.6825 (ttpt) REVERT: A 564 GLN cc_start: 0.6642 (mt0) cc_final: 0.6070 (mt0) REVERT: A 779 GLN cc_start: 0.7907 (tt0) cc_final: 0.7159 (tp40) REVERT: A 921 LYS cc_start: 0.7495 (tppt) cc_final: 0.6889 (mttp) REVERT: A 987 PRO cc_start: 0.7546 (Cg_exo) cc_final: 0.7180 (Cg_endo) REVERT: A 1092 GLU cc_start: 0.7230 (pt0) cc_final: 0.6933 (pt0) REVERT: B 30 ASN cc_start: 0.6411 (t0) cc_final: 0.6149 (t0) REVERT: B 53 ASP cc_start: 0.6708 (t0) cc_final: 0.6192 (t0) REVERT: B 68 ILE cc_start: 0.3645 (OUTLIER) cc_final: 0.3328 (pp) REVERT: B 153 MET cc_start: 0.0775 (tpp) cc_final: -0.1437 (mtt) REVERT: B 338 PHE cc_start: 0.4394 (OUTLIER) cc_final: 0.3706 (m-10) REVERT: B 654 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6508 (tm-30) REVERT: B 719 THR cc_start: 0.8790 (OUTLIER) cc_final: 0.8407 (t) REVERT: B 735 SER cc_start: 0.8340 (t) cc_final: 0.7856 (p) REVERT: B 740 MET cc_start: 0.8099 (tpp) cc_final: 0.7787 (tpp) REVERT: B 814 LYS cc_start: 0.6927 (OUTLIER) cc_final: 0.6659 (mmtp) REVERT: B 990 GLU cc_start: 0.7172 (mt-10) cc_final: 0.6521 (tm-30) REVERT: B 1010 GLN cc_start: 0.7658 (mm110) cc_final: 0.6801 (pt0) REVERT: C 82 MET cc_start: -0.0204 (mmm) cc_final: -0.0685 (ptp) REVERT: D 51 THR cc_start: 0.8042 (OUTLIER) cc_final: 0.7498 (t) REVERT: D 153 MET cc_start: -0.0600 (mtm) cc_final: -0.1146 (mmp) REVERT: D 237 ARG cc_start: 0.7019 (mtt180) cc_final: 0.6467 (mtm180) REVERT: D 361 CYS cc_start: 0.5659 (OUTLIER) cc_final: 0.4532 (p) REVERT: D 535 LYS cc_start: 0.6758 (mttt) cc_final: 0.6359 (mtmm) REVERT: D 551 VAL cc_start: 0.5333 (OUTLIER) cc_final: 0.5096 (t) REVERT: D 565 PHE cc_start: 0.4836 (m-80) cc_final: 0.4567 (m-10) REVERT: D 604 THR cc_start: 0.7901 (m) cc_final: 0.7615 (m) REVERT: D 735 SER cc_start: 0.8260 (t) cc_final: 0.7779 (p) REVERT: D 854 LYS cc_start: 0.4640 (ptpt) cc_final: 0.4115 (tptt) REVERT: D 978 ASN cc_start: 0.7492 (t0) cc_final: 0.6692 (m-40) REVERT: D 983 ARG cc_start: 0.6701 (ttp80) cc_final: 0.6361 (ttm170) REVERT: D 988 GLU cc_start: 0.7344 (tp30) cc_final: 0.7083 (mt-10) REVERT: D 1002 GLN cc_start: 0.7472 (tt0) cc_final: 0.7226 (tt0) REVERT: D 1038 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8175 (tppt) outliers start: 88 outliers final: 48 residues processed: 266 average time/residue: 1.1135 time to fit residues: 360.6821 Evaluate side-chains 237 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 178 time to evaluate : 3.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 964 LYS Chi-restraints excluded: chain D residue 974 SER Chi-restraints excluded: chain D residue 985 ASP Chi-restraints excluded: chain D residue 1038 LYS Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 316 optimal weight: 1.9990 chunk 288 optimal weight: 6.9990 chunk 308 optimal weight: 2.9990 chunk 185 optimal weight: 3.9990 chunk 134 optimal weight: 0.5980 chunk 241 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 chunk 278 optimal weight: 20.0000 chunk 291 optimal weight: 5.9990 chunk 306 optimal weight: 0.9980 chunk 202 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN B 66 HIS B 134 GLN B1002 GLN D 641 ASN D 762 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 28167 Z= 0.190 Angle : 0.558 9.061 38337 Z= 0.285 Chirality : 0.045 0.277 4469 Planarity : 0.004 0.054 4917 Dihedral : 4.842 56.621 4687 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.14 % Favored : 96.78 % Rotamer: Outliers : 2.66 % Allowed : 16.06 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.14), residues: 3413 helix: 1.99 (0.20), residues: 686 sheet: 0.09 (0.16), residues: 902 loop : -1.07 (0.14), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 436 HIS 0.003 0.001 HIS D1064 PHE 0.033 0.001 PHE D 541 TYR 0.019 0.001 TYR B1067 ARG 0.006 0.000 ARG B 466 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 187 time to evaluate : 2.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 34 MET cc_start: 0.1985 (tmt) cc_final: 0.1705 (mpt) REVERT: A 70 VAL cc_start: 0.1605 (OUTLIER) cc_final: 0.1393 (m) REVERT: A 127 VAL cc_start: 0.6930 (OUTLIER) cc_final: 0.6582 (m) REVERT: A 191 GLU cc_start: 0.5931 (mt-10) cc_final: 0.5602 (mp0) REVERT: A 359 SER cc_start: 0.7205 (p) cc_final: 0.6822 (m) REVERT: A 528 LYS cc_start: 0.7689 (ttmm) cc_final: 0.6835 (ttpt) REVERT: A 564 GLN cc_start: 0.6746 (mt0) cc_final: 0.6146 (mt0) REVERT: A 779 GLN cc_start: 0.7900 (tt0) cc_final: 0.7151 (tp-100) REVERT: A 921 LYS cc_start: 0.7505 (tppt) cc_final: 0.6894 (mttp) REVERT: A 987 PRO cc_start: 0.7552 (Cg_exo) cc_final: 0.7185 (Cg_endo) REVERT: A 1092 GLU cc_start: 0.7235 (pt0) cc_final: 0.6940 (pt0) REVERT: B 30 ASN cc_start: 0.6333 (t0) cc_final: 0.6079 (t0) REVERT: B 53 ASP cc_start: 0.6674 (t0) cc_final: 0.6172 (t0) REVERT: B 68 ILE cc_start: 0.3574 (OUTLIER) cc_final: 0.3274 (pp) REVERT: B 153 MET cc_start: 0.0803 (tpp) cc_final: -0.1366 (mtt) REVERT: B 338 PHE cc_start: 0.4403 (OUTLIER) cc_final: 0.3710 (m-10) REVERT: B 654 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6572 (tm-30) REVERT: B 719 THR cc_start: 0.8775 (OUTLIER) cc_final: 0.8413 (t) REVERT: B 735 SER cc_start: 0.8347 (t) cc_final: 0.7862 (p) REVERT: B 740 MET cc_start: 0.8095 (tpp) cc_final: 0.7754 (tpp) REVERT: B 814 LYS cc_start: 0.6893 (OUTLIER) cc_final: 0.6640 (mmtp) REVERT: B 990 GLU cc_start: 0.7155 (mt-10) cc_final: 0.6515 (tm-30) REVERT: B 1010 GLN cc_start: 0.7662 (mm110) cc_final: 0.6787 (pt0) REVERT: C 82 MET cc_start: -0.0228 (mmm) cc_final: -0.0719 (ptp) REVERT: D 51 THR cc_start: 0.8011 (OUTLIER) cc_final: 0.7493 (t) REVERT: D 126 VAL cc_start: 0.6362 (OUTLIER) cc_final: 0.5962 (t) REVERT: D 153 MET cc_start: -0.0515 (mtm) cc_final: -0.1077 (mmp) REVERT: D 237 ARG cc_start: 0.7065 (mtt180) cc_final: 0.6487 (mtm180) REVERT: D 361 CYS cc_start: 0.5677 (OUTLIER) cc_final: 0.4555 (p) REVERT: D 535 LYS cc_start: 0.6812 (mttt) cc_final: 0.6403 (mtmm) REVERT: D 551 VAL cc_start: 0.5269 (OUTLIER) cc_final: 0.5055 (t) REVERT: D 565 PHE cc_start: 0.4752 (m-80) cc_final: 0.4504 (m-10) REVERT: D 604 THR cc_start: 0.7915 (m) cc_final: 0.7646 (m) REVERT: D 735 SER cc_start: 0.8260 (t) cc_final: 0.7790 (p) REVERT: D 854 LYS cc_start: 0.4608 (ptpt) cc_final: 0.4077 (tptt) REVERT: D 978 ASN cc_start: 0.7582 (t0) cc_final: 0.6784 (m-40) REVERT: D 983 ARG cc_start: 0.6672 (ttp80) cc_final: 0.6344 (ttm170) REVERT: D 1002 GLN cc_start: 0.7516 (tt0) cc_final: 0.7265 (tt0) REVERT: D 1038 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8177 (tppt) outliers start: 80 outliers final: 50 residues processed: 257 average time/residue: 1.1004 time to fit residues: 343.9446 Evaluate side-chains 245 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 183 time to evaluate : 2.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 974 SER Chi-restraints excluded: chain D residue 985 ASP Chi-restraints excluded: chain D residue 1038 LYS Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 325 optimal weight: 3.9990 chunk 198 optimal weight: 2.9990 chunk 154 optimal weight: 0.3980 chunk 226 optimal weight: 0.8980 chunk 341 optimal weight: 3.9990 chunk 314 optimal weight: 3.9990 chunk 272 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 210 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 216 optimal weight: 2.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A1088 HIS B 66 HIS D 146 HIS D 641 ASN D 978 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6759 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 28167 Z= 0.283 Angle : 0.625 9.574 38337 Z= 0.319 Chirality : 0.047 0.270 4469 Planarity : 0.005 0.058 4917 Dihedral : 5.291 59.090 4687 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.10 % Favored : 95.81 % Rotamer: Outliers : 2.86 % Allowed : 16.16 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.14), residues: 3413 helix: 1.65 (0.20), residues: 696 sheet: 0.01 (0.16), residues: 906 loop : -1.09 (0.14), residues: 1811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 436 HIS 0.005 0.001 HIS D1064 PHE 0.031 0.002 PHE D 541 TYR 0.028 0.002 TYR A1067 ARG 0.004 0.001 ARG A 577 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 194 time to evaluate : 2.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 34 MET cc_start: 0.2265 (tmt) cc_final: 0.1977 (mpt) REVERT: A 273 ARG cc_start: 0.3821 (mmm-85) cc_final: 0.3044 (mmt-90) REVERT: A 316 SER cc_start: 0.7333 (OUTLIER) cc_final: 0.7059 (p) REVERT: A 359 SER cc_start: 0.7201 (p) cc_final: 0.6817 (m) REVERT: A 528 LYS cc_start: 0.7660 (ttmm) cc_final: 0.6810 (ttpt) REVERT: A 564 GLN cc_start: 0.6827 (mt0) cc_final: 0.6174 (mt0) REVERT: A 779 GLN cc_start: 0.7942 (tt0) cc_final: 0.7153 (tp40) REVERT: A 921 LYS cc_start: 0.7611 (tppt) cc_final: 0.6971 (mtmp) REVERT: A 987 PRO cc_start: 0.7587 (Cg_exo) cc_final: 0.7241 (Cg_endo) REVERT: A 1092 GLU cc_start: 0.7258 (pt0) cc_final: 0.6961 (pt0) REVERT: B 30 ASN cc_start: 0.6187 (t0) cc_final: 0.5893 (t0) REVERT: B 53 ASP cc_start: 0.6728 (t0) cc_final: 0.6168 (t0) REVERT: B 68 ILE cc_start: 0.3743 (OUTLIER) cc_final: 0.3434 (pp) REVERT: B 153 MET cc_start: 0.0951 (tpp) cc_final: -0.1286 (mtt) REVERT: B 338 PHE cc_start: 0.4644 (OUTLIER) cc_final: 0.3963 (m-10) REVERT: B 654 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6600 (tm-30) REVERT: B 735 SER cc_start: 0.8339 (t) cc_final: 0.7842 (p) REVERT: B 740 MET cc_start: 0.8081 (tpp) cc_final: 0.7790 (tpp) REVERT: B 814 LYS cc_start: 0.6974 (OUTLIER) cc_final: 0.6714 (mmtp) REVERT: B 1010 GLN cc_start: 0.7653 (mm110) cc_final: 0.6828 (pt0) REVERT: C 82 MET cc_start: -0.0355 (mmm) cc_final: -0.0865 (ptp) REVERT: D 28 TYR cc_start: 0.6691 (OUTLIER) cc_final: 0.4726 (m-80) REVERT: D 51 THR cc_start: 0.8029 (OUTLIER) cc_final: 0.7523 (t) REVERT: D 52 GLN cc_start: 0.7494 (OUTLIER) cc_final: 0.6686 (mm-40) REVERT: D 153 MET cc_start: -0.0559 (mtm) cc_final: -0.1031 (mmm) REVERT: D 237 ARG cc_start: 0.7169 (mtt180) cc_final: 0.6521 (mtm180) REVERT: D 361 CYS cc_start: 0.5751 (OUTLIER) cc_final: 0.4638 (p) REVERT: D 535 LYS cc_start: 0.6905 (mttt) cc_final: 0.6458 (mtmm) REVERT: D 619 GLU cc_start: 0.7587 (mp0) cc_final: 0.7228 (mp0) REVERT: D 735 SER cc_start: 0.8228 (t) cc_final: 0.7677 (p) REVERT: D 854 LYS cc_start: 0.4723 (ptpt) cc_final: 0.4190 (tptt) REVERT: D 978 ASN cc_start: 0.7580 (t0) cc_final: 0.6727 (m-40) REVERT: D 983 ARG cc_start: 0.6803 (ttp80) cc_final: 0.6532 (ttm170) REVERT: D 1002 GLN cc_start: 0.7482 (tt0) cc_final: 0.7236 (tt0) outliers start: 86 outliers final: 53 residues processed: 263 average time/residue: 1.0988 time to fit residues: 353.5309 Evaluate side-chains 247 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 185 time to evaluate : 2.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain D residue 28 TYR Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 750 SER Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 974 SER Chi-restraints excluded: chain D residue 985 ASP Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 289 optimal weight: 9.9990 chunk 83 optimal weight: 0.7980 chunk 250 optimal weight: 20.0000 chunk 40 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 272 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 279 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 239 optimal weight: 0.6980 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS B 66 HIS ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 641 ASN D 762 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.224809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.162016 restraints weight = 32970.197| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 1.98 r_work: 0.3370 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.182 28167 Z= 0.335 Angle : 0.757 59.200 38337 Z= 0.409 Chirality : 0.048 0.441 4469 Planarity : 0.005 0.058 4917 Dihedral : 5.294 59.106 4687 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.98 % Favored : 95.93 % Rotamer: Outliers : 2.56 % Allowed : 16.76 % Favored : 80.68 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.14), residues: 3413 helix: 1.63 (0.20), residues: 696 sheet: 0.00 (0.16), residues: 906 loop : -1.10 (0.14), residues: 1811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 436 HIS 0.005 0.001 HIS A1064 PHE 0.030 0.002 PHE D 541 TYR 0.027 0.002 TYR A1067 ARG 0.005 0.000 ARG D 44 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8750.27 seconds wall clock time: 158 minutes 18.09 seconds (9498.09 seconds total)